Input file for intervals argument

apchumangenomicsapchumangenomics University College CorkMember

Hi All, I am currently running MuTect 2 on my files. However, this is taking quite a deal of time per tumour/ normal pair analysis. I have read that using the intervals argument would decrease runtime. However, I am unsure what such a file looks like or where to get one. My data is derived from exome sequencing with exome capture being performed using Sureselect Human All Exon V5. I have downloaded the files: S04380110_AllTracks.bed, S04380110_Covered.bed, S04380110_Padded.bed, S04380110_Regions.bed, S04380110_Targets.txt and S04380110_Regions.bed. Not sure if any of these are correct file to use. Thanks for any help.

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